I wanted to change the margins so the icons look normal with the wallpaper I have. I had to move the icons after every reboot or after I restarted X.
Edit the file /usr/sbin/fixPuppyPin
change the line - NEWRIGHTX=`expr $SCREENX - 32` to NEWRIGHTX=`expr $SCREENX - 64` to bring the margins in another 32.
Now if I could just fix that darn bottom...